Avogadro 0.9.7

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Avogadro 0.9.7 was released on 18 July 2009. This is the eighth of our final beta series before Avogadro 1.0.0 is released. Please help us by providing feedback. New beta releases are expected roughly once per month until the 1.0.0 release. You can download this release here.

What's New

The following list includes some of the changes since Avogadro 0.9.6. This is a bug fix release with some feature enhancements since our last release.

General

  • Detached 3D views - multiple simultaneous views of the molecule.
  • Updated user interface and icons.
  • Improved display type configuration.
  • Updated translations.
  • More bugs found and fixed.

Rendering

  • Orbital and surface display types merged into surface display.
  • Cartoon display now has reasonable default colors.

Extensions

  • Improved surface rendering dialog, reduced to one dialog.

Python

  • Fixes to work with SIP 4.8.

Dependencies

  1. Eigen 2.0.3 http://eigen.tuxfamily.org/ -- for compiling only.
  2. OpenBabel 2.2.2 or later http://openbabel.org
  3. CMake 2.6.0 or later http://www.cmake.org
  4. Qt 4.5.1 or later http://www.trolltech.com
  5. Boost 1.35 or later http://www.boost.org/ -- for Python support (optional).
  6. GLEW 1.5.0 or later http://glew.sourceforge.net/ -- for GLSL support (optional)

Building

untar the source

tar xvjf avogadro-0.9.7.tar.bz2

make the build directory

cd avogadro-0.9.7
mkdir build

configure

cd build
cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_GLSL=ON -DENABLE_PYTHON=ON ..
CMake takes a few optional parameters:
  • -DCMAKE_INSTALL_PREFIX= : specify the installation prefix (default /usr/local)
  • -DOPENBABEL2_LIBRARIES= : specify the OpenBabel2 libraries
  • -DOPENBABEL2_INCLUDE_DIR : specify the OpenBabel2 include directory
  • -DEIGEN_INCLUDE_DIR : specify the Eigen include directory
  • -DCMAKE_BUILD_TYPE : specify the build type (Debug, Release etc)
  • -DENABLE_GLSL : set to ON to enable, or OFF to disable GLSL support.
  • -DENABLE_PYTHON : set to ON to enable, or OFF to disable Python support.
  • -DENABLE_RPATH: set to ON to install binaries with relative RPaths (no need to set LD_LIBRARY_PATH).
  • -DENABLE_UPDATE_CHECKER: set to ON to enable checks for updated versions over the network - Linux distributions might want to disable this to avoid user confusion.

For more information see the CMake website; http://www.cmake.org/

build

make

install

make install

Known Issues & Limitations

This release is a beta release and is intended to gain feedback and interest in the project.

The code currently expects to be editing one 3D molecule per file with one coordinate set. This means:

  • Editing a multi-molecule file will only edit the first molecule. Saving will overwrite all records except the first.
  • Saving to a 2D format will not necessarily produce correct 2D stereochemistry.

Tools / Building

  • Several builder features are not implemented, including:
    • Crystal structure builder
    • Carbon Nanotube builder
    • Z-matrix editor (early version committed - needs more work)

Interface

  • Export graphics will only save the current resolution in the window in bitmap form.

Troubleshooting

Problem: OpenBabel2 / Eigen libraries are not found.

Solution: The most likely the cause of this problem is non-standard install locations. Additionally, the detection system for finding libraries and includes is not flawless. The most likely remedy is to manually specify the library location and include directory for the package using the cmake arguments specified above.